@jbrowse/plugin-bed 2.6.1 → 2.6.3

package/src/BigBedAdapter/index.ts

@@ -1,16 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(
-    () =>
-      new AdapterType({
-        name: 'BigBedAdapter',
-        displayName: 'BigBed adapter',
-        configSchema,
-        getAdapterClass: () => import('./BigBedAdapter').then(r => r.default),
-      }),
-  )
-}

package/src/__snapshots__/index.test.ts.snap

@@ -1,3 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`plugin in a stock JBrowse 1`] = `{}`;

package/src/index.test.ts

@@ -1,16 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { getSnapshot } from 'mobx-state-tree'
-import ThisPlugin from '.'
-
-test('plugin in a stock JBrowse', () => {
-  const pluginManager = new PluginManager([new ThisPlugin()])
-  pluginManager.createPluggableElements()
-  pluginManager.configure()
-  expect(() => pluginManager.addPlugin(new ThisPlugin())).toThrow(
-    /JBrowse already configured, cannot add plugins/,
-  )
-
-  const BigBedAdapter = pluginManager.getAdapterType('BigBedAdapter')
-  const config = BigBedAdapter.configSchema.create({ type: 'BigBedAdapter' })
-  expect(getSnapshot(config)).toMatchSnapshot()
-})

package/src/index.ts

@@ -1,133 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import BigBedAdapterF from './BigBedAdapter'
-import BedpeAdapterF from './BedpeAdapter'
-import BedTabixAdapterF from './BedTabixAdapter'
-import BedAdapterF from './BedAdapter'
-import { FileLocation } from '@jbrowse/core/util/types'
-import {
-  getFileName,
-  makeIndex,
-  makeIndexType,
-  AdapterGuesser,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
-
-export default class BedPlugin extends Plugin {
-  name = 'BedPlugin'
-
-  install(pluginManager: PluginManager) {
-    BigBedAdapterF(pluginManager)
-    BedAdapterF(pluginManager)
-    BedpeAdapterF(pluginManager)
-    BedTabixAdapterF(pluginManager)
-    pluginManager.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
-          const regexGuess = /\.(bb|bigbed)$/i
-          const adapterName = 'BigBedAdapter'
-          const fileName = getFileName(file)
-          const obj = {
-            type: adapterName,
-            bigBedLocation: file,
-          }
-
-          if (regexGuess.test(fileName) && !adapterHint) {
-            return obj
-          } else if (adapterHint === adapterName) {
-            return obj
-          }
-          return adapterGuesser(file, index, adapterHint)
-        }
-      },
-    )
-
-    pluginManager.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
-          const regexGuess = /\.bedpe\.gz$/i
-          const adapterName = 'BedpeAdapter'
-          const fileName = getFileName(file)
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              bedpeLocation: file,
-            }
-          }
-          return adapterGuesser(file, index, adapterHint)
-        }
-      },
-    )
-
-    pluginManager.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
-          const regexGuess = /\.bed\.b?gz$/i
-          const adapterName = 'BedTabixAdapter'
-          const fileName = getFileName(file)
-          const indexName = index && getFileName(index)
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              bedGzLocation: file,
-              index: {
-                location: index || makeIndex(file, '.tbi'),
-                indexType: makeIndexType(indexName, 'CSI', 'TBI'),
-              },
-            }
-          }
-          return adapterGuesser(file, index, adapterHint)
-        }
-      },
-    )
-
-    pluginManager.addToExtensionPoint(
-      'Core-guessAdapterForLocation',
-      (adapterGuesser: AdapterGuesser) => {
-        return (
-          file: FileLocation,
-          index?: FileLocation,
-          adapterHint?: string,
-        ) => {
-          const regexGuess = /\.bed$/i
-          const adapterName = 'BedAdapter'
-          const fileName = getFileName(file)
-          if (regexGuess.test(fileName) || adapterHint === adapterName) {
-            return {
-              type: adapterName,
-              bedLocation: file,
-            }
-          }
-          return adapterGuesser(file, index, adapterHint)
-        }
-      },
-    )
-
-    pluginManager.addToExtensionPoint(
-      'Core-guessTrackTypeForLocation',
-      (trackTypeGuesser: TrackTypeGuesser) => {
-        return (adapterName: string) => {
-          if (adapterName === 'BedpeAdapter') {
-            return 'VariantTrack'
-          }
-          return trackTypeGuesser(adapterName)
-        }
-      },
-    )
-  }
-}

package/src/util.ts

@@ -1,180 +0,0 @@
-import { SimpleFeature, Feature } from '@jbrowse/core/util'
-import BED from '@gmod/bed'
-
-export function ucscProcessedTranscript(feature: Feature) {
-  const children = feature.children()
-  // split the blocks into UTR, CDS, and exons
-  const thickStart = feature.get('thickStart')
-  const thickEnd = feature.get('thickEnd')
-
-  if (!thickStart && !thickEnd) {
-    return feature
-  }
-
-  const blocks: Feature[] = children
-    ? children
-        .filter(child => child.get('type') === 'block')
-        .sort((a, b) => a.get('start') - b.get('start'))
-    : []
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  const newChildren: Record<string, any> = []
-  blocks.forEach(block => {
-    const start = block.get('start')
-    const end = block.get('end')
-    if (thickStart >= end) {
-      // left-side UTR
-      const prime = feature.get('strand') > 0 ? 'five' : 'three'
-      newChildren.push({
-        type: `${prime}_prime_UTR`,
-        start,
-        end,
-      })
-    } else if (thickStart > start && thickStart < end && thickEnd >= end) {
-      // UTR | CDS
-      const prime = feature.get('strand') > 0 ? 'five' : 'three'
-      newChildren.push(
-        {
-          type: `${prime}_prime_UTR`,
-          start,
-          end: thickStart,
-        },
-        {
-          type: 'CDS',
-          start: thickStart,
-          end,
-        },
-      )
-    } else if (thickStart <= start && thickEnd >= end) {
-      // CDS
-      newChildren.push({
-        type: 'CDS',
-        start,
-        end,
-      })
-    } else if (thickStart > start && thickStart < end && thickEnd < end) {
-      // UTR | CDS | UTR
-      const leftPrime = feature.get('strand') > 0 ? 'five' : 'three'
-      const rightPrime = feature.get('strand') > 0 ? 'three' : 'five'
-      newChildren.push(
-        {
-          type: `${leftPrime}_prime_UTR`,
-          start,
-          end: thickStart,
-        },
-        {
-          type: `CDS`,
-          start: thickStart,
-          end: thickEnd,
-        },
-        {
-          type: `${rightPrime}_prime_UTR`,
-          start: thickEnd,
-          end,
-        },
-      )
-    } else if (thickStart <= start && thickEnd > start && thickEnd < end) {
-      // CDS | UTR
-      const prime = feature.get('strand') > 0 ? 'three' : 'five'
-      newChildren.push(
-        {
-          type: `CDS`,
-          start,
-          end: thickEnd,
-        },
-        {
-          type: `${prime}_prime_UTR`,
-          start: thickEnd,
-          end,
-        },
-      )
-    } else if (thickEnd <= start) {
-      // right-side UTR
-      const prime = feature.get('strand') > 0 ? 'three' : 'five'
-      newChildren.push({
-        type: `${prime}_prime_UTR`,
-        start,
-        end,
-      })
-    }
-  })
-  const newData = Object.fromEntries(
-    feature.tags().map(tag => [tag, feature.get(tag)]),
-  )
-  newData.subfeatures = newChildren
-  newData.type = 'mRNA'
-  newData.uniqueId = feature.id()
-  delete newData.chromStarts
-  delete newData.chromStart
-  delete newData.chromEnd
-  delete newData.chrom
-  delete newData.blockStarts
-  delete newData.blockSizes
-  delete newData.blockCount
-  delete newData.thickStart
-  delete newData.thickEnd
-  return new SimpleFeature({
-    data: newData,
-    id: feature.id(),
-  })
-}
-
-function defaultParser(fields: string[], line: string) {
-  return Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]))
-}
-
-export function featureData(
-  line: string,
-  colRef: number,
-  colStart: number,
-  colEnd: number,
-  scoreColumn: string,
-  parser: BED,
-  uniqueId: string,
-  names?: string[],
-) {
-  const l = line.split('\t')
-  const refName = l[colRef]
-  const start = +l[colStart]
-  const colSame = colStart === colEnd ? 1 : 0
-
-  const end = +l[colEnd] + colSame
-  const data = names
-    ? defaultParser(names, line)
-    : parser.parseLine(line, { uniqueId })
-
-  const { blockCount, blockSizes, blockStarts, chromStarts } = data
-
-  if (blockCount) {
-    const starts = chromStarts || blockStarts || []
-    const sizes = blockSizes
-    const blocksOffset = start
-    data.subfeatures = []
-
-    for (let b = 0; b < blockCount; b += 1) {
-      const bmin = (starts[b] || 0) + blocksOffset
-      const bmax = bmin + (sizes[b] || 0)
-      data.subfeatures.push({
-        uniqueId: `${uniqueId}-${b}`,
-        start: bmin,
-        end: bmax,
-        type: 'block',
-      })
-    }
-  }
-
-  if (scoreColumn) {
-    data.score = +data[scoreColumn]
-  }
-  delete data.chrom
-  delete data.chromStart
-  delete data.chromEnd
-  const f = new SimpleFeature({
-    ...data,
-    start,
-    end,
-    refName,
-    uniqueId,
-  })
-  return f.get('thickStart') ? ucscProcessedTranscript(f) : f
-}